rs55659625

chr14-93246298-TAAAA-Tchr14-93246298-TAAAA-TAchr14-93246298-TAAAA-TAAchr14-93246298-TAAAA-TAAAchr14-93246298-TAAAA-TAAAAAchr14-93246298-TAAAA-TAAAAAAchr14-93246298-TAAAA-TAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001002860.4(BTBD7):c.2122-16_2122-13del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00024 in 1,207,038 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00024 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BTBD7 NM_001002860.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

BTBD7 (HGNC:18269): (BTB domain containing 7) Predicted to be involved in regulation of branching involved in salivary gland morphogenesis. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTBD7	NM_001002860.4	c.2122-16_2122-13del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000334746.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTBD7	ENST00000334746.10	c.2122-16_2122-13del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001002860.4	P1
BTBD7	ENST00000554565.5	c.1069-16_1069-13del		splice_polypyrimidine_tract_variant, intron_variant		1
BTBD7	ENST00000553975.1	c.967-16_967-13del		splice_polypyrimidine_tract_variant, intron_variant		2
BTBD7	ENST00000355125.3	c.*743-16_*743-13del		splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 142556 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000657 AC: 71 AN: 108090 Hom.: 0 AF XY: 0.000751 AC XY: 44 AN XY: 58568

Gnomad AFR exome AF: 0.000796

Gnomad AMR exome AF: 0.000527

Gnomad ASJ exome AF: 0.000970

Gnomad EAS exome AF: 0.000413

Gnomad SAS exome AF: 0.00138

Gnomad FIN exome AF: 0.0000918

Gnomad NFE exome AF: 0.000681

Gnomad OTH exome AF: 0.000894

GnomAD4 exome AF: 0.000240 AC: 290 AN: 1207038 Hom.: 0 AF XY: 0.000273 AC XY: 160 AN XY: 585610

Gnomad4 AFR exome AF: 0.000149

Gnomad4 AMR exome AF: 0.000231

Gnomad4 ASJ exome AF: 0.000348

Gnomad4 EAS exome AF: 0.000229

Gnomad4 SAS exome AF: 0.00139

Gnomad4 FIN exome AF: 0.000222

Gnomad4 NFE exome AF: 0.000185

Gnomad4 OTH exome AF: 0.000282

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 142556 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 69148

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs55659625; hg19: chr14-93712644;